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Table 4 Properties of hrpG-regulated genes in X. campestris pv raphani strain CFBP 5828R grown in MOKA medium

From: Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome

Locus Taga Gene names Fold change (hrpG*/EV)b Product PIP boxc Conservation in other Xc d
Genes of the hrp gene cluster and encoding putative type III secreted proteins   
3860 xopR 14 Xanthomonas outer protein R yes 13
5760 xopAR 220 Xanthomonas outer protein AR - 12
17460 xopAC 127 Xanthomonas outer protein AC - 12
19470 avrXccA2 34 AvrXccA2 - 7
30660 - 16 hypothetical protein - 12
30670 - 53 hypothetical protein - 12
30680 - 8 hypothetical protein - 12
30720 bgl1 6 beta-glucosidase - 12
30730 - 473 ncRNA yes 13
30740 - 80 hypothetical protein - 13
30750 xopP 68 Xanthomonas outer protein P yes 13
30760 - 6 ncRNA - 13
30770 xopAL1 359 Xanthomonas outer protein AL1 yes 13
30780 - 221 hypothetical protein (+) 8
30790 - 298 hypothetical protein (+) 13
30800 - 222 hypothetical protein (+) 13
30810 - 60 hypothetical protein (+) 11
30820 - 66 hypothetical protein (+) 13
30840 hpa2 885 type III secretion-system related transglycosylase yes 13
30850 hpa1/xopA 504 Hpa1, Xanthomonas outer protein A yes 13
30860 hrcC 81 HrcC protein - 13
30870 hrcT 142 HrcT protein (+) 13
30880 hrpB7 67 HrpB7 protein (+) 13
30890 hrcN 129 type III secretion system ATPase (+) 13
30900 - 217 type III secretion system protein HrpB (+) 13
30910 hrpB4 168 type III secretion system protein (+) 13
30920 hrcJ 218 HrcJ protein (+) 13
30930 hrpB2 303 HrpB2 protein (+) 13
30940 hrpB1 307 HrpB1 protein yes 13
30950 hrcU 113 type III secretion system protein HrcU yes 13
30960 hrcV 63 type III secretory pathway component (+) 13
30970 hpaC 116 HpaC protein (+) 13
30980 hrcQ 133 HrcQ protein yes 13
30990 - 208 type III secretion system protein (+) 13
31000 - 147 hypothetical protein (+) 13
31010 hpaA 173 HpaA protein (+) 13
31020 hrcD 356 HrcD protein yes 13
31030 hrpD6 304 HrpD6 protein (+) 13
31040 hrpE 345 type III secretion system pilus protein (+) 13
31050 hpaB 454 type III secretion system export control protein (+) 13
31060 hrpW 128 glycosylhydrolase-like type III secretion system protein (+) 13
31070 xopF1 70 hypothetical protein = XopF1 (+) 13
31080 hpa3 148 Hpa3 protein, type III secretion system yes 5
31090 - 32   yes 3
31100 - 12 ncRNA - 3
31110 - 79 AutoIPR: IPR008490:Transposase InsH, N-terminal; (+) 3
31120 - 14 ncRNA (+) 3
31130 xopAT 11 Xanthomonas outer protein AT yes 3
31140 xopAD 25 Shikimate kinase, Xanthomonas outer protein AD - 5
31160 - 34   - 5
31170 hrpF 66 type III secretion system host membrane insertion protein - 13
31180 - 7   - 10
31690 hrpX 35 AraC family transcriptional regulator = hrpX - 13
31720 hrpG 89 transcriptional regulator HrpG - 13
31730 - 7 ncRNA - 13
42660 xopL 45 Xanthomonas outer protein L yes 9
Other genes   
430 - 10 methyltransferase yes 13
1770 dctP 6 dicarboxylate transport system, periplasmic substate binding component - 13
1780 dctQ 6 dicarboxylate transport system, small permease component - 13
1790 dctM 6 dicarboxylate transport system, large permease component - 13
1800 xylB3 6 xylan 1,4-beta-xylosidase/alpha-N-arabinofuranosidase - 13
4520 - 20 transcrictional regulator, MarR family - 13
4530 - 20 hypothetical protein - 11
4540 - 15 hypothetical protein - 12
4550 tsr2 9 membrane-anchored chemotaxis sensory transducer - 12
4870 pcaK 30 4-hydroxybenzoate/protocatachuate MFS transporter - 13
4880 - 6 hypothetical protein - 13
5010 - 8 oxygenase subunit - 13
5020 - 12 oxygenase subunit - 13
5530 - 13 hypothetical protein - 13
5540 - 18   - 13
5660 virK 32 hypothetical protein - 13
5770 - 49   - 12
5790 - 44 AutoIPR: IPR008490:Transposase InsH, N-terminal; - 1
5800 - 43   - 11
5810 - 33   - 11
6120 - 8 hypothetical protein - 13
8610 pglA1 90 polygalacturonase yes 13
9460 celS2 10 cellulase/xyloglucan hydrolase yes 10
9760 - 28 hypothetical protein - 8
9930 leuC 8 isopropylmalate isomerase large subunit - 13
9940 leuD 9 isopropylmalate isomerase small subunit - 13
9950 ubiE2 8 ubiquinone/menaquinone biosynthesis methyltransferase - 13
9960 leuB 8 3-isopropylmalate dehydrogenase - 13
11650 - 20   - 1
12120 - 13 hypothetical protein - 3
12940 - 55 hypothetical protein - 13
13330 - 59 hypothetical protein - 13
13340 - 431   - 13
13350 - 188 hypothetical protein - 10
13360 - 450 hypothetical protein - 13
13400 - 24 secreted lipase yes 13
14380 - 7 ncRNA - 13
14820 - 0,11 Endoproteinase Arg-C (C-terminal fragment) - 13
16210 - 9 cysteine protease yes 7
16450 - 8 serine endopeptidase - 13
16460 - 19 hypothetical protein - 13
16470 - 99 serine endopeptidase - 13
16480 - 41 ncRNA - 13
17350 - 56 Metallopeptidase - 13
19460 - 29 peptidase - 13
19650 - 14 hypothetical protein - 13
20940 pglA2 14 polygalacturonase yes 13
20950 - 30 putative pectate lyase (+) 1
20960 - 54 putative Serine/cysteine peptidase protein yes 1
20970 - 10 AutoIPR: IPR000070:Pectinesterase, catalytic; IPR011050:Pectin lyase fold/virulence factor; - 1
23600 - 8 hypothetical protein - 13
23610 - 116 Metallopeptidase - 13
26170 - 31 TonB-dependent outer membrane receptor precursor yes 13
26550 - 46 MFS glucose importer - 13
26750 - 16 hypothetical protein - 13
26760 rpoE4 8 RNA polymerase ECF-type sigma factor - 13
26770 - 7 hypothetical protein - 13
26780 - 8 Subtilase family serine protease - 13
26790 - 7 ABC transporter heme permease CcmC - 13
26810 - 6 cytochrome c-type biogenesis protein CcmE - 13
26820 - 6 C-type cytochrome biogenesis membrane protein CcmF - 13
26830 - 8 Thiol:disulfide interchange protein (c-type cytochrome biogenesis protein CcmG) - 13
26840 - 5 Formate-dependent nitrite reductase complex nrfFG subunit precursor. - 13
27610 - 15 hypothetical protein - 13
28890 cah2 9 carbonate dehydratase - 13
28970 - 21 transcriptional regulator, MarR family - 13
29010 - 6 hypothetical protein - 13
29100 - 0,16 Major facilitator superfamily protein - 13
29120 oprN5 0,14 outer membrane efflux protein - 13
29130 - 0,19 transcriptional regulator, MarR family - 13
29740 - 7 TonB-dependent outer membrane receptor precursor - 13
32520 - 56 hypothetical protein - 13
32540 - 53 ncRNA - 13
33090 - 9 hypothetical protein - 13
33100 - 11 hypothetical protein - 13
35670 - 13 transcriptional regulator, LysR family (+) 13
35680 ligA 34 protocatechuate 4,5-dioxygenase subunit alpha (+) 13
35690 ligB 54 protocatechuate 4,5-dioxygenase subunit beta yes 13
37110 - 0,11 hypothetical protein - 13
37120 - 0,18 hypothetical protein - 13
37610 pel3 0,14 pectate lyase - 13
40980 - 30 disulfide-isomerase - 13
42070 - 34 Acid phosphatase precursor - 13
42650 - 7 integrase - 12
45310 - 20 hypothetical protein - 12
  1. aLocus tag number prefix: XCRCFBP5828_m001
  2. bOnly genes with both a fold change higher than five and an adjusted P-value lower than 0.001 are shown. EV empty vector
  3. cyes: Presence of PIP box (TTCGB-N15-TTCGB) in the proper orientation in front of the gene. (+): Presence of a PIP-box consensus in the proper orientation in front of a possible operon
  4. dNumbers indicate how many of the 13 Xc genomes contain at least one homologue of the considered genes as determined by OrthoMCL for protein-coding genes and blastn for ncRNAs